public QueryResult<ReportedVariant> index(String study, String token) throws IOException, ClinicalVariantException, CatalogException { DBIterator<ClinicalAnalysis> clinicalAnalysisDBIterator = clinicalAnalysisManager.iterator(study, new Query(), QueryOptions.empty(), token); while (clinicalAnalysisDBIterator.hasNext()) { ClinicalAnalysis clinicalAnalysis = clinicalAnalysisDBIterator.next(); for (Interpretation interpretation : clinicalAnalysis.getInterpretations()) { interpretation.getInterpretation().getAttributes().put("OPENCGA_CLINICAL_ANALYSIS", clinicalAnalysis); this.clinicalVariantEngine.insert(interpretation.getInterpretation(), database); } } return null; }